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ARS Home » Midwest Area » Ames, Iowa » National Laboratory for Agriculture and The Environment » Agroecosystems Management Research » Research » Research Project #422830


Location: Agroecosystems Management Research

2014 Annual Report

Objective 1: Assess conservation practices and develop conservation planning tools that can improve agricultural water quality in the Midwest. Sub-objectives: 1) Develop and evaluate practices for reducing surface water contaminants in artificially drained landscapes; 2) Evaluate practices to reduce runoff and sediment losses from urban sites; and 3) Develop and evaluate tools to optimize placement of conservation practices within Midwest watersheds for improved environmental benefits. Objective 2: Determine the effects of climate, land use, and conservation practices on hydrology and water quality in agricultural watersheds. Sub-objectives: 1) Quantify hydrologic and water quality dynamics and their responses to changes in land use, conservation, and climatic conditions in Iowa watersheds; 2) Determine effects of landscape hydrology on soils and water quality in naturally and artificially drained landscapes; and 3) Map stream channel and bank movement in context with riparian land use and geomorphic setting to identify opportunities for restoring riparian ecosystems. Objective 3: Determine the fate and transport of pathogens and trace emergent compounds in agricultural soils and streams. Sub-objectives: 1) Determine transport pathways and environmental residence times of zoonotic pathogens associated with animal agriculture and the effects of management practices on those processes; 2) Determine transport pathways and environmental residence times of veterinary pharmaceuticals and the effects of management practices on those processes; 3) Determine if exposure to trace antibiotic residues in soil or stream sediment affects the persistence of antibiotic resistant bacteria and resistance genes; and 4) As part of the LTAR network, and in concert with similar long-term, land-based research infrastructure in Upper Mississippi River Basin region, use the UMRB LTAR to improve the observational capabilities and data accessibility of the LTAR network, to support research to sustain or enhance agricultural production and environmental quality in agroecosystems characteristic of the Upper Mississippi River Basin, as per the LTAR site responsibilities and other information outlined in the 2012 USDA Long- LTAR Network Request for Information (RFI) to which the location successfully responded, and the LTAR Shared Research Strategy, a living document that serves as a roadmap for LTAR implementation. Participation in the LTAR network includes research and data management in support of the ARS GRACEnet and/or Livestock GRACEnet projects.

This project will conduct research to investigate the effects of agricultural management practices at field and watershed scales, the dynamics of watershed hydrology, and fundamental processes relevant to contaminant behavior in watersheds. Under the first objective, field studies will evaluate practices that can reduce loss of nitrate-nitrogen from cropped fields. These practices include resaturated buffers and bioreactors, practices that intercept tile drainage, and two practices that can reduce N loss to tiles, namely side-dressing of anhydrous ammonia and fall-planted cover crops. Bioreactor denitrification capacities will be assessed with microbiological assessments, and modeling studies will be conducted to extend experimental results on conservation practices to other areas of the Midwest. Research will be conducted to develop and evaluate watershed analyses to place conservation practices for improved water quality outcomes and determine how those strategies can be regionalized across the Midwest. Conservation needs also exist in urban environments and an experiment to determine how compost amendments can reduce urban runoff will be carried out. The second objective will be conducted in three Iowa watersheds, where stream monitoring will provide databases for watershed modeling studies, and for testing hypotheses about impacts of changes in climate and land use on water quality and hydrology. This research will be supported by efforts to identify field-scale patterns of hydrology and water quality, and better understand how new mapping techniques using Light Detection and Ranging (LiDAR) data can assist in understanding field hydrology, river corridor management, and targeting of conservation practices. The third objective will employ a mix of laboratory and field studies to evaluate environmental transport and residence times of pathogens and veterinary pharmaceuticals in soils and streams, and determine if exposure to trace antibiotic residues in soil or stream sediment affect the persistence of antibiotic resistant bacteria and antibiotic resistance genes. A breadth of watershed monitoring, controlled experiments in field and laboratory, and modeling techniques will be employed in the research. Publications, tools for conservation planning, and databases available to other scientists will be produced. Results are intended to enable agriculture to better manage water resources for multiple needs, particularly in the Upper Mississippi River basin.

Progress Report
Objective 1.1. Research on saturated buffers continues on two main sites and 13 additional sites installed with support from a Natural Resource Conservation Service (NRCS) Conservation Innovation Grant and funds from USDA-Economic Research Service. The Iowa saturated buffers are intercepting about 50% of the tile drainage water leaving the fields with all nitrate contained in the intercepted water removed in the buffer. New research documents that nitrogen use efficiency of commercial nitrogen fertilizer is greatest when sidedressed, lower when applied pre-plant, and lowest when applied in the fall before growing corn. Guidelines for agricultural systems modeling parameterization were developed as part of an initiative with the Agricultural and Biological Engineers (ASABE). A manuscript based on this work was submitted to the Transactions of the ASABE in April (2014). We are also working to improve the rye cover crop routine within the Root Zone Water Quality Model (RZWQM) agricultural model using long term field data collected in previous studies. Objective 1.2. Research on urban conservation practices was continued. Studies of water movement through experimental columns were conducted to help determine appropriate soil mixes for urban bioretention cells (e.g., rain gardens). Rainfall simulation studies were conducted to compare runoff and retention of soil water between compost amended and non-amended lawns. Objective 1.3. Research was initiated to determine differences in volumes tile drainage among soil types and landscape positions using existing plot studies. Objective 2.1. Watershed monitoring efforts in the South Fork of the Iowa River Walnut Creek (north), and Walnut Creek (south) were continued. Data are being processed for contributions to the Sustaining the Earth's Watershed Agricultural Research Database System (STEWARDS) database. Analysis of the rainfall patterns for Iowa and the surrounding Midwest states show a change in seasonality of precipitation with more rain events in the spring period (April through June) with more intense storms and less frequent storms. Water balance models are being evaluated for cropping systems typical of the Midwest. A project to evaluate the effectiveness of surface inlet filters for removal of sediment and nutrients was initiated in the South Fork of the Iowa River. Activities under the Long Term Agroecosystem Research (LTAR) network are being initiated; research planning meetings have been held with other locations in the Upper Mississippi River Basin LTAR (Morris and St Paul, MN and University of Wisconsin-Platteville’s Pioneer Farm). Objective 2.2 Soil water and shallow groundwater monitoring was continued as part of an effort to identify patterns of water movement and water quality as affected by soil type and landscape position. Objective 2.3 Imagery based on detailed topography obtained using Light Detecting and Ranging (LiDAR) systems, aerial photography, and land use were combined to provide summary data describing streambank movement resulting from a major flood in 2008. Objective 3. Monitoring of E coli and Enterococcus in stream water in the South Fork of the Iowa River (SFIR) and Neil Smith Wildlife Refuge (NSWR) watersheds have been completed. These watersheds have also been monitored for the antibiotics tylosin and sulfamethazine in water and sediment. Preliminary studies have been completed and new, more sensitive analytical methods have been developed. Also, an alternative in-situ sampling method (POCIS) is being evaluated in SFIR. The transport of tylosin and tylosin-resistance genes (erm) in tile drainage were investigated in replicated plot study. Tylosin dissipated quickly under field conditions and transport of resistant microorganisms (as erm genes) was not greatly affected by manure application. We constructed a modified Salmonella strain that lacks virulence genes to use in laboratory survival studies. This strain is also resistant to antibiotics allowing selective plating for measuring survival. Concentrations of Salmonella in stream water are quite low and standard selective media are not effective.

1. Saturated buffers for nitrate removal. Streamside buffers are a proven practice for removing nitrate from both overland flow and shallow groundwater before it can enter the stream. However, in landscapes with tile drainage, most of the subsurface flow leaving farmers’ fields is passed through the buffers in tiles leaving little opportunity for nitrate removal in buffers. We showed that re-routing a fraction of field tile drainage from a 25 ac field through a riparian buffer as subsurface flow removed more than 250 lbs of nitrate-nitrogen each year before it entered surface waters. Saturated buffers are a promising management practice for improving surface water quality within tile-drained, agricultural landscapes and wide-scale adoption could remove millions of pounds of nitrate before it enters the Nation’s surface waters.

2. Antibiotic-resistance genes in drainage water. There is broad concern that antibiotic use in animal agriculture results in increased levels of antibiotic-resistant bacteria and reduced antibiotic effectiveness. ARS and Iowa State University scientists conducted a multi-year, systematic study of the fate and transport of macrolide antibiotic resistance (erm) genes in soil and drainage water in fields treated with swine manure. Although the abundance of the resistance genes in soil was increased after manure application, transport of these genes in drainage water was similar to that observed in water from fields not receiving manure during two years with below-average drainage volumes. But in the one year with above-average drainage, erm gene abundance was increased with manure application. In the second year following manure application, resistance gene abundance in soil continued to decline reaching levels that were comparable to those in soil without manure treatment. The results indicate that swine manure injected into soil can result in greater off-site transport of resistance genes, which informs producers and the public about risks associated with these common agricultural practices.

3. Cropping system impacts on nutrient concentrations in soil water. Nutrient losses associated with annual row crops in the Midwest might be reduced through changes in cropping systems. An ARS scientist in Ames, Iowa, collaborated with an Iowa State University faculty member in an eight-year study to compare nutrient concentrations in soil water beneath cropping rotations including a two-year corn and soybean rotation, a three-year corn-soybean-oat/clover rotation, and a four-year corn-soybean-oat/alfalfa-alfalfa rotation. While nitrate losses beneath perennial crops like alfalfa have been shown small, this research showed that benefit can be extended to the following corn crop when alfalfa is grown in a rotational system. There was also evidence to show that phosphorus losses can be reduced by using perennial crops in rotation with annual crops. The four-year rotation is most feasible for farms that integrate crop and livestock production. The finding that crop rotations can moderate losses of both nitrogen and phosphorus to receiving waters is of interest to the agricultural and conservation communities.

4. Patterns of calcium carbonate accumulation surrounding topographic depressions. Lime (calcium carbonate) accumulates at edges of topographic depressions that are common in some glacial landscapes, as ponded water transports the lime out and up from the depressions. Researchers in Ames, Iowa, showed the lime was concentrated in the low - slope area at zones where the depression curled outward into embayments, rather than where there were peninsulas into the depression. Although this study examined lime, other chemicals that are only slightly dissolved in water could accumulate in a similar way around depressions. This information is primarily of interest to soil surveyors and scientists concerned with water quality and chemical transport through landscapes and cropped fields that have topographic depressions. Eventually, results could be used to vary fertilizer and agrichemical applications in and near farmed depressions in order to minimize the risk of off-site transport.

Review Publications
Zhou, X., Helmers, M.J., Asbjornsen, H., Kolka, R.K., Tomer, M.D., Cruse, R.M. 2014. Nutrient removal by prairie filter strips in agricultural landscapes. Journal of Soil and Water Conservation. 69(1):54-64.
Tomer, M.D., Liebman, M. 2014. Nutrients in soil water under three rotational cropping systems, Iowa, USA. Agriculture, Ecosystems and Environment. 186:105-114.
Logsdon, S.D., James, D.E. 2014. Closed depression topography Harps soil, revisited. Soil Horizons. 55(2):1-7. Available at:
Palmer, J.A., Schilling, K.E., Isenhart, T.M., Schultz, R.C., Tomer, M.D. 2014. Streambank erosion rates and loads within a single watershed: Bridging the gap between temporal and spatial scales. Geomorphology. 209:66-78.
Jaynes, D.B., Isenhart, T.M. 2014. Reconnecting tile drainage to riparian buffer hydrology for enhanced nitrate removal. Journal of Environmental Quality. 43:631-638.
Xu, J., Ma, X., Logsdon, S.D., Horton, R. 2014. FDR probe structure influence on the soil dielectric spectrum measurement. Transactions of the Chinese Agricultural Machinery. 45(1):102-107.
Malone, R.W., Nolan, B.T., Ma, L., Kanwar, R., Peterson, C., Heilman, P. 2013. Tillage and application rate affects atrazine transport to subsurface drainage with macropore flow: Evaluation of RZWQM using a long-term field study. Agricultural Water Management. 132:10-22.
Moriasi, D.N., Gowda, P., Arnold, J.G., Mulla, D.J., Ale, S., Steiner, J.L., Tomer, M.D. 2013. Evaluation of the Hooghoudt and Kirkham tile drain equations in SWAT to simulate tile flow and nitrate-nitrogen. Journal of Environmental Quality. 42:1699-1710.
Garder, J., Moorman, T.B., Soupir, M. 2014. Transport and persistence of tylosin-resistant enterococci, erm genes, and tylosin in soil and drainage water from fields receiving swine manure. Journal of Environmental Quality. Available at: 43:1484-1493.
Jaynes, D.B. 2013. Nitrate loss in subsurface drainage and corn yield as affected by timing of sidedress nitrogen. Agricultural Water Management. 130:52-60. Available:
Fang, Q.X., Ma, L., Yu, Q., Hu, C.S., Li, X.X., Malone, R.W., Ahuja, L.R. 2013. Quantifying climate and management effects on regional crop yield and N leaching in the North China Plain. Journal of Environmental Quality. 42:1466–1479.
Christianson, L., Helmers, M., Bhandari, A., Moorman, T.B. 2012. Internal hydraulics of an agricultural drainage denitrification bioreactor. Ecological Engineering. 298-307.
Carstens, K.L., Gross, A.D., Moorman, T.B., Coats, J.R. 2013. Sorption and photo degradation processes govern distribution of sulfamethazine in freshwater-sediment microcosms. Environmental Science and Technology. 10877-10883.
Tomer, M.D., Beeson, P.C., Meek, D.W., Moriasi, D.N., Rossi, C.G., Sadeghi, A.M. 2013. Evaluating simulations of daily discharge from large watersheds using autoregression and an index of flashiness. Transactions of the ASABE. 56(4):1317-1326.